Immediately following graduation, Kerr eschewed a minor-league baseball contract and began teaching mathematics at the Rowe School in Johnstown, Pennsylvania.  The following year he moved to the Johnstown High School.  His began his coaching in Johnstown and when he moved to the Pittsburgh area, he came to the attention of Glenn "Pop" Warner, then at the University of Pittsburgh.  In 1914, Kerr left what had already been an extended career as a mathematics teacher and joined Warner's staff at Pitt.  He was to coach football for the rest of his life, becoming one of the most influential college football coaches in history as he did so.

He began his head coaching as interim coach at Stanford in 1922 on behalf of Warner, who could not contractually move west until 1924.  He then became head coach at Washington and Jefferson in 1926.  In 1931, he found his coaching home at Colgate University, where he served for the next eighteen seasons.  His teams there were outstanding as Kerr built on the Warner double wing with an array of precise lateral "razzle-dazzle" offensive inventions.  The record he built at Colgate was remarkable - including the famous "unbeaten, untied, unscored upon, and uninvited" 1932 team which was 9-0 with a points total of 264-0 and not considered good enough for the Rose Bowl.  He left Colgate due to mandatory retirement age rules in 1946 but coached on till 1950 at Lebanon Valley College.  The Colgate football stadium is named for him and in 1964 that university invested him with an honorary degree of doctor of laws.  He was also a driving force behind the Shrine East West Game held each year at Stanford to raise funds for children's hospitals.  He was head coach of the East squad from 1927 to 1950 and general manager of the East's annual effort following that.  Considered, along with Amos Alonzo Stagg and his mentor Warner, as one of the three men who developed college football into what it became, he was installed as a charter member of the Football Hall of Fame. 

Andy Kerr - nicknamed "the canny Scot"- had married Mary Keister and the couple had two sons.  He retired to his home in Hamilton, New York.  Wintering in Tucson, Arizona, as was his custom, he suffered a heart attack and died on February 17, 1969.  Andrew Kerr was ninety years old.